applications/staticProps/StaticProps.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
#include <iostream>
#include <fstream>
#include <string>

#include "brains/SimCreator.hpp"
#include "brains/SimInfo.hpp"
#include "io/DumpReader.hpp"
#include "utils/simError.h"

#include "applications/staticProps/StaticPropsCmd.h"
#include "applications/staticProps/StaticAnalyser.hpp"
#include "applications/staticProps/GofR.hpp"
#include "applications/staticProps/GofZ.hpp"
#include "applications/staticProps/GofRZ.hpp"
#include "applications/staticProps/GofRAngle.hpp"
#include "applications/staticProps/GofAngle2.hpp"
#include "applications/staticProps/GofXyz.hpp"
#include "applications/staticProps/TwoDGofR.hpp"
#include "applications/staticProps/P2OrderParameter.hpp"
#include "applications/staticProps/BondOrderParameter.hpp"
#include "applications/staticProps/BOPofR.hpp"
#include "applications/staticProps/RippleOP.hpp"
#include "applications/staticProps/SCDOrderParameter.hpp"
#include "applications/staticProps/DensityPlot.hpp"
#include "applications/staticProps/ObjectCount.hpp"
#include "applications/staticProps/RhoZ.hpp"
#include "applications/staticProps/pAngle.hpp"
#include "applications/staticProps/BondAngleDistribution.hpp"
#include "applications/staticProps/NanoVolume.hpp"
#include "applications/staticProps/NanoLength.hpp"
#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
#include "applications/staticProps/Hxy.hpp"
#endif
#include "applications/staticProps/RhoR.hpp"
#include "applications/staticProps/AngleR.hpp"
#include "applications/staticProps/TetrahedralityParam.hpp"
#include "applications/staticProps/TetrahedralityParamZ.hpp"
using namespace OpenMD;

int main(int argc, char* argv[]){
  
  
  gengetopt_args_info args_info;
  
  //parse the command line option
  if (cmdline_parser (argc, argv, &args_info) != 0) {
    exit(1) ;
  }
  
  //get the dumpfile name
  std::string dumpFileName = args_info.input_arg;
  std::string sele1;
  std::string sele2;
  
  // check the first selection argument, or set it to the environment
  // variable, or failing that, set it to "select all"
  
  if (args_info.sele1_given) {
    sele1 = args_info.sele1_arg;
  } else {
    char*  sele1Env= getenv("SELECTION1");
    if (sele1Env) {
      sele1 = sele1Env;
    } else {
      sele1 = "select all";
    }
  }
  
  // check the second selection argument, or set it to the environment
  // variable, or failing that, set it to "select all"
  
  if (args_info.sele2_given) {
    sele2 = args_info.sele2_arg;
  } else {
    char* sele2Env = getenv("SELECTION1");
    if (sele2Env) {
      sele2 = sele2Env;            
    } else { 
      //It seems likely (from previous discussions) that if sele2 is not specified, then the default behavior
      //should not be 'select all' but rather what is already intended for sele1
      //JRM 8/22/12
      sele2 = sele1;
      //sele2 = "select all";
    }
  }
  
  
  // Problems if sele1 wasn't specified, but 
  // if (!args_info.scd_given) {
  //       sprintf( painCave.errMsg,
  //                "neither --sele1 option nor $SELECTION1 is set");
  //       painCave.severity = OPENMD_ERROR;
  //       painCave.isFatal = 1;
  //       simError();
  //     }
  //   }
  
  // Problems if sele1 wasn't specified
  
  //     if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given)  {
  //       sprintf( painCave.errMsg,
  //                "neither --sele2 option nor $SELECTION1 is set");
  //       painCave.severity = OPENMD_ERROR;
  //       painCave.isFatal = 1;
  //       simError();        
  //     }
  //   }
  
  bool batchMode;
  if (args_info.scd_given){
    if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
      batchMode = false;
    } else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
      if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
        sprintf( painCave.errMsg,
                 "below conditions are not satisfied:\n"
                 "0 <= begin && 0<= end && begin <= end-2\n");
        painCave.severity = OPENMD_ERROR;
        painCave.isFatal = 1;
        simError();                    
      }
      batchMode = true;        
    } else{
      sprintf( painCave.errMsg,
               "either --sele1, --sele2, --sele3 are specified,"
               " or --molname, --begin, --end are specified\n");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();        
      
    }
  }
  
  //parse md file and set up the system
  SimCreator creator;
  std::cout << "dumpFile = " << dumpFileName << "\n";
  SimInfo* info = creator.createSim(dumpFileName);

  RealType maxLen;
  RealType zmaxLen;
  if (args_info.length_given) {
    maxLen = args_info.length_arg;
    if (args_info.zlength_given){
      zmaxLen = args_info.zlength_arg;
    }
  } else {
    Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
    maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
    zmaxLen = hmat(2,2);    
  }    
  
  StaticAnalyser* analyser;
  if (args_info.gofr_given){
    analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen, 
                       args_info.nbins_arg);        
  } else if (args_info.gofz_given) {
    analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
                       args_info.nbins_arg);
  } else if (args_info.r_z_given) {
    analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen, 
                          args_info.nbins_arg, args_info.nbins_z_arg);
  } else if (args_info.r_theta_given) {
    analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen, 
                              args_info.nbins_arg, args_info.nanglebins_arg);
  } else if (args_info.r_omega_given) {
    analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen, 
                              args_info.nbins_arg, args_info.nanglebins_arg);
  } else if (args_info.theta_omega_given) {
    analyser  = new GofAngle2(info, dumpFileName, sele1, sele2, 
                              args_info.nanglebins_arg);
  } else if (args_info.gxyz_given) {
    if (args_info.refsele_given) {
      analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg, 
                           maxLen, args_info.nbins_arg);        
    } else {
      sprintf( painCave.errMsg,
               "--refsele must set when --gxyz is used");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();  
    }
  } else if (args_info.twodgofr_given){
    if (args_info.dz_given) {
      analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen, 
                             args_info.dz_arg, args_info.nbins_arg);        
    } else {
      sprintf( painCave.errMsg,
               "A slab width (dz) must be specified when calculating TwoDGofR");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }    
  } else if (args_info.p2_given) {
    if (args_info.sele1_given) {     
      if (args_info.sele2_given) 
        analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
      else 
        analyser  = new P2OrderParameter(info, dumpFileName, sele1);
    } else {
      sprintf( painCave.errMsg,
               "At least one selection script (--sele1) must be specified when calculating P2 order parameters");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
  } else if (args_info.rp2_given){
    analyser = new RippleOP(info, dumpFileName, sele1, sele2);
  } else if (args_info.bo_given){
    if (args_info.rcut_given) {
      analyser = new BondOrderParameter(info, dumpFileName, sele1, 
                                        args_info.rcut_arg, 
                                        args_info.nbins_arg);
    } else {
      sprintf( painCave.errMsg,
               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
    
  } else if (args_info.tet_param_given) {
    if (args_info.rcut_given) {   
      analyser = new TetrahedralityParam(info, dumpFileName, sele1, 
                                         args_info.rcut_arg, 
                                         args_info.nbins_arg);
    } else {
      sprintf( painCave.errMsg,
               "A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
  } else if (args_info.tet_param_z_given) {
    if (args_info.rcut_given) {   
      analyser = new TetrahedralityParamZ(info, dumpFileName, sele1, 
                                         args_info.rcut_arg, 
                                         args_info.nbins_arg);
    } else {
      sprintf( painCave.errMsg,
               "A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
  } else if (args_info.bor_given){
    if (args_info.rcut_given) {
      analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
                            args_info.nbins_arg, maxLen);
    } else {
      sprintf( painCave.errMsg,
               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
  } else if (args_info.bad_given){
    if (args_info.rcut_given) {
      analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg,
                                           args_info.nbins_arg);
    } else {
      sprintf( painCave.errMsg,
               "A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
      }
  } else if (args_info.scd_given) {
    if (batchMode) {
      analyser  = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg, 
                                        args_info.begin_arg, args_info.end_arg);
    } else{
      std::string sele3 = args_info.sele3_arg;
      analyser  = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
    }
  }else if (args_info.density_given) {
    analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
                              args_info.nbins_arg);  
  } else if (args_info.count_given) {
    analyser = new ObjectCount(info, dumpFileName, sele1 );
  } else if (args_info.slab_density_given) {
    analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
  } else if (args_info.p_angle_given) {
    analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg);
#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
  }else if (args_info.hxy_given) {
    analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg, 
                       args_info.nbins_y_arg, args_info.nbins_arg);
#endif
  }else if (args_info.rho_r_given) {
    if (args_info.radius_given){
      analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
    }else{
      sprintf( painCave.errMsg,
               "A particle radius (radius) must be specified when calculating Rho(r)");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
  } else if (args_info.hullvol_given) {
    analyser = new NanoVolume(info, dumpFileName, sele1);
  } else if (args_info.rodlength_given) {
    analyser = new NanoLength(info, dumpFileName, sele1);
  } else if (args_info.angle_r_given) {
    analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
  }
    
  if (args_info.output_given) {
    analyser->setOutputName(args_info.output_arg);
  }
  if (args_info.step_given) {
    analyser->setStep(args_info.step_arg);
  }
 
  analyser->process();
  
  delete analyser;    
  delete info;

  return 0;   
}

Revision:	1785
Committed:	Wed Aug 22 18:43:27 2012 UTC (12 years, 8 months ago) by jmichalk
File size:	13729 byte(s)
Log Message:	Trunk: The changes in this commit are confined to applications/staticProps and for the most part deal with a misspelling of initialize. The one other change took place in StaticProps.cpp and deals with the default treatment of sele2. It had previously been set to 'select all' which seems to go against what would be desired by not specifying it with regard to proper operations of many of the analysis programs ( g of r's especially)
#	User	Rev	Content
1	gezelter	507	/*
2	tim	310	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	tim	310	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	tim	310	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31	gezelter	1390	*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	gezelter	1782	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	tim	310	*/
42
43			#include <iostream>
44			#include <fstream>
45			#include <string>
46
47			#include "brains/SimCreator.hpp"
48			#include "brains/SimInfo.hpp"
49			#include "io/DumpReader.hpp"
50			#include "utils/simError.h"
51
52	tim	311	#include "applications/staticProps/StaticPropsCmd.h"
53	tim	543	#include "applications/staticProps/StaticAnalyser.hpp"
54	tim	311	#include "applications/staticProps/GofR.hpp"
55	xsun	1213	#include "applications/staticProps/GofZ.hpp"
56	gezelter	1440	#include "applications/staticProps/GofRZ.hpp"
57	tim	311	#include "applications/staticProps/GofRAngle.hpp"
58			#include "applications/staticProps/GofAngle2.hpp"
59			#include "applications/staticProps/GofXyz.hpp"
60	gezelter	1454	#include "applications/staticProps/TwoDGofR.hpp"
61	tim	543	#include "applications/staticProps/P2OrderParameter.hpp"
62	gezelter	1039	#include "applications/staticProps/BondOrderParameter.hpp"
63	chuckv	1128	#include "applications/staticProps/BOPofR.hpp"
64	xsun	980	#include "applications/staticProps/RippleOP.hpp"
65	tim	544	#include "applications/staticProps/SCDOrderParameter.hpp"
66	tim	545	#include "applications/staticProps/DensityPlot.hpp"
67	gezelter	1513	#include "applications/staticProps/ObjectCount.hpp"
68	tim	840	#include "applications/staticProps/RhoZ.hpp"
69	gezelter	1413	#include "applications/staticProps/pAngle.hpp"
70	chuckv	1180	#include "applications/staticProps/BondAngleDistribution.hpp"
71			#include "applications/staticProps/NanoVolume.hpp"
72	gezelter	1585	#include "applications/staticProps/NanoLength.hpp"
73	gezelter	957	#if defined(HAVE_FFTW_H) \|\| defined(HAVE_DFFTW_H) \|\| defined(HAVE_FFTW3_H)
74	xsun	955	#include "applications/staticProps/Hxy.hpp"
75	gezelter	956	#endif
76	chuckv	1091	#include "applications/staticProps/RhoR.hpp"
77	kstocke1	1522	#include "applications/staticProps/AngleR.hpp"
78			#include "applications/staticProps/TetrahedralityParam.hpp"
79	gezelter	1782	#include "applications/staticProps/TetrahedralityParamZ.hpp"
80	gezelter	1390	using namespace OpenMD;
81	tim	310
82			int main(int argc, char* argv[]){
83
84	gezelter	1513
85			gengetopt_args_info args_info;
86
87			//parse the command line option
88			if (cmdline_parser (argc, argv, &args_info) != 0) {
89			exit(1) ;
90			}
91
92			//get the dumpfile name
93			std::string dumpFileName = args_info.input_arg;
94			std::string sele1;
95			std::string sele2;
96
97			// check the first selection argument, or set it to the environment
98			// variable, or failing that, set it to "select all"
99
100			if (args_info.sele1_given) {
101			sele1 = args_info.sele1_arg;
102			} else {
103			char* sele1Env= getenv("SELECTION1");
104			if (sele1Env) {
105			sele1 = sele1Env;
106			} else {
107			sele1 = "select all";
108			}
109			}
110
111			// check the second selection argument, or set it to the environment
112			// variable, or failing that, set it to "select all"
113
114			if (args_info.sele2_given) {
115			sele2 = args_info.sele2_arg;
116			} else {
117			char* sele2Env = getenv("SELECTION1");
118			if (sele2Env) {
119			sele2 = sele2Env;
120			} else {
121	jmichalk	1785	//It seems likely (from previous discussions) that if sele2 is not specified, then the default behavior
122			//should not be 'select all' but rather what is already intended for sele1
123			//JRM 8/22/12
124			sele2 = sele1;
125			//sele2 = "select all";
126	gezelter	1513	}
127			}
128
129
130			// Problems if sele1 wasn't specified, but
131			// if (!args_info.scd_given) {
132			// sprintf( painCave.errMsg,
133			// "neither --sele1 option nor $SELECTION1 is set");
134			// painCave.severity = OPENMD_ERROR;
135			// painCave.isFatal = 1;
136			// simError();
137			// }
138			// }
139
140			// Problems if sele1 wasn't specified
141
142			// if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given) {
143			// sprintf( painCave.errMsg,
144			// "neither --sele2 option nor $SELECTION1 is set");
145			// painCave.severity = OPENMD_ERROR;
146			// painCave.isFatal = 1;
147			// simError();
148			// }
149			// }
150
151			bool batchMode;
152			if (args_info.scd_given){
153			if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
154			batchMode = false;
155			} else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
156			if (args_info.begin_arg < 0 \|\| args_info.end_arg < 0 \|\| args_info.begin_arg > args_info.end_arg-2) {
157			sprintf( painCave.errMsg,
158			"below conditions are not satisfied:\n"
159			"0 <= begin && 0<= end && begin <= end-2\n");
160			painCave.severity = OPENMD_ERROR;
161			painCave.isFatal = 1;
162			simError();
163			}
164			batchMode = true;
165			} else{
166			sprintf( painCave.errMsg,
167			"either --sele1, --sele2, --sele3 are specified,"
168			" or --molname, --begin, --end are specified\n");
169			painCave.severity = OPENMD_ERROR;
170			painCave.isFatal = 1;
171			simError();
172
173			}
174			}
175
176			//parse md file and set up the system
177			SimCreator creator;
178			std::cout << "dumpFile = " << dumpFileName << "\n";
179			SimInfo* info = creator.createSim(dumpFileName);
180	tim	310
181	gezelter	1513	RealType maxLen;
182			RealType zmaxLen;
183			if (args_info.length_given) {
184			maxLen = args_info.length_arg;
185			if (args_info.zlength_given){
186			zmaxLen = args_info.zlength_arg;
187	chuckv	1445	}
188	gezelter	1513	} else {
189			Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
190			maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
191			zmaxLen = hmat(2,2);
192			}
193	kstocke1	1522
194	gezelter	1513	StaticAnalyser* analyser;
195			if (args_info.gofr_given){
196			analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
197	kstocke1	1522	args_info.nbins_arg);
198	gezelter	1513	} else if (args_info.gofz_given) {
199			analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
200	kstocke1	1522	args_info.nbins_arg);
201	gezelter	1513	} else if (args_info.r_z_given) {
202			analyser = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
203	kstocke1	1522	args_info.nbins_arg, args_info.nbins_z_arg);
204	gezelter	1513	} else if (args_info.r_theta_given) {
205			analyser = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
206	kstocke1	1522	args_info.nbins_arg, args_info.nanglebins_arg);
207	gezelter	1513	} else if (args_info.r_omega_given) {
208			analyser = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
209	kstocke1	1522	args_info.nbins_arg, args_info.nanglebins_arg);
210	gezelter	1513	} else if (args_info.theta_omega_given) {
211			analyser = new GofAngle2(info, dumpFileName, sele1, sele2,
212	kstocke1	1522	args_info.nanglebins_arg);
213	gezelter	1513	} else if (args_info.gxyz_given) {
214			if (args_info.refsele_given) {
215			analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg,
216	kstocke1	1522	maxLen, args_info.nbins_arg);
217	gezelter	1039	} else {
218	gezelter	1513	sprintf( painCave.errMsg,
219	kstocke1	1522	"--refsele must set when --gxyz is used");
220	gezelter	1513	painCave.severity = OPENMD_ERROR;
221			painCave.isFatal = 1;
222			simError();
223	tim	310	}
224	gezelter	1513	} else if (args_info.twodgofr_given){
225			if (args_info.dz_given) {
226			analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen,
227	kstocke1	1522	args_info.dz_arg, args_info.nbins_arg);
228	chuckv	1445	} else {
229	gezelter	1513	sprintf( painCave.errMsg,
230	kstocke1	1522	"A slab width (dz) must be specified when calculating TwoDGofR");
231	gezelter	1513	painCave.severity = OPENMD_ERROR;
232			painCave.isFatal = 1;
233			simError();
234	kstocke1	1522	}
235	gezelter	1513	} else if (args_info.p2_given) {
236	gezelter	1542	if (args_info.sele1_given) {
237			if (args_info.sele2_given)
238			analyser = new P2OrderParameter(info, dumpFileName, sele1, sele2);
239			else
240			analyser = new P2OrderParameter(info, dumpFileName, sele1);
241			} else {
242			sprintf( painCave.errMsg,
243			"At least one selection script (--sele1) must be specified when calculating P2 order parameters");
244			painCave.severity = OPENMD_ERROR;
245			painCave.isFatal = 1;
246			simError();
247			}
248	gezelter	1513	} else if (args_info.rp2_given){
249			analyser = new RippleOP(info, dumpFileName, sele1, sele2);
250			} else if (args_info.bo_given){
251			if (args_info.rcut_given) {
252			analyser = new BondOrderParameter(info, dumpFileName, sele1,
253	kstocke1	1522	args_info.rcut_arg,
254			args_info.nbins_arg);
255	gezelter	1513	} else {
256			sprintf( painCave.errMsg,
257	kstocke1	1522	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
258	gezelter	1513	painCave.severity = OPENMD_ERROR;
259			painCave.isFatal = 1;
260			simError();
261	tim	544	}
262	kstocke1	1522
263			} else if (args_info.tet_param_given) {
264			if (args_info.rcut_given) {
265			analyser = new TetrahedralityParam(info, dumpFileName, sele1,
266			args_info.rcut_arg,
267			args_info.nbins_arg);
268			} else {
269			sprintf( painCave.errMsg,
270			"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
271			painCave.severity = OPENMD_ERROR;
272			painCave.isFatal = 1;
273			simError();
274			}
275	gezelter	1782	} else if (args_info.tet_param_z_given) {
276			if (args_info.rcut_given) {
277			analyser = new TetrahedralityParamZ(info, dumpFileName, sele1,
278			args_info.rcut_arg,
279			args_info.nbins_arg);
280			} else {
281			sprintf( painCave.errMsg,
282			"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
283			painCave.severity = OPENMD_ERROR;
284			painCave.isFatal = 1;
285			simError();
286			}
287	gezelter	1513	} else if (args_info.bor_given){
288			if (args_info.rcut_given) {
289			analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
290	kstocke1	1522	args_info.nbins_arg, maxLen);
291	chuckv	1445	} else {
292	gezelter	1513	sprintf( painCave.errMsg,
293	kstocke1	1522	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
294	gezelter	1513	painCave.severity = OPENMD_ERROR;
295			painCave.isFatal = 1;
296			simError();
297			}
298			} else if (args_info.bad_given){
299			if (args_info.rcut_given) {
300			analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg,
301	kstocke1	1522	args_info.nbins_arg);
302	gezelter	1513	} else {
303			sprintf( painCave.errMsg,
304	kstocke1	1522	"A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
305	gezelter	1513	painCave.severity = OPENMD_ERROR;
306			painCave.isFatal = 1;
307			simError();
308	kstocke1	1522	}
309	gezelter	1513	} else if (args_info.scd_given) {
310			if (batchMode) {
311			analyser = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
312	kstocke1	1522	args_info.begin_arg, args_info.end_arg);
313	gezelter	1513	} else{
314			std::string sele3 = args_info.sele3_arg;
315			analyser = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
316			}
317			}else if (args_info.density_given) {
318			analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
319	kstocke1	1522	args_info.nbins_arg);
320	gezelter	1513	} else if (args_info.count_given) {
321			analyser = new ObjectCount(info, dumpFileName, sele1 );
322			} else if (args_info.slab_density_given) {
323			analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
324			} else if (args_info.p_angle_given) {
325			analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg);
326	gezelter	957	#if defined(HAVE_FFTW_H) \|\| defined(HAVE_DFFTW_H) \|\| defined(HAVE_FFTW3_H)
327	gezelter	1513	}else if (args_info.hxy_given) {
328			analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
329	kstocke1	1522	args_info.nbins_y_arg, args_info.nbins_arg);
330	gezelter	956	#endif
331	gezelter	1513	}else if (args_info.rho_r_given) {
332			if (args_info.radius_given){
333			analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
334			}else{
335			sprintf( painCave.errMsg,
336	kstocke1	1522	"A particle radius (radius) must be specified when calculating Rho(r)");
337	gezelter	1513	painCave.severity = OPENMD_ERROR;
338			painCave.isFatal = 1;
339			simError();
340	chuckv	1091	}
341	kstocke1	1522	} else if (args_info.hullvol_given) {
342	gezelter	1513	analyser = new NanoVolume(info, dumpFileName, sele1);
343	gezelter	1585	} else if (args_info.rodlength_given) {
344			analyser = new NanoLength(info, dumpFileName, sele1);
345	kstocke1	1522	} else if (args_info.angle_r_given) {
346			analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
347	gezelter	1513	}
348	kstocke1	1522
349	gezelter	1513	if (args_info.output_given) {
350			analyser->setOutputName(args_info.output_arg);
351			}
352			if (args_info.step_given) {
353			analyser->setStep(args_info.step_arg);
354			}
355	gezelter	1782
356	gezelter	1513	analyser->process();
357	kstocke1	1522
358	gezelter	1513	delete analyser;
359			delete info;
360	tim	310
361	gezelter	1513	return 0;
362	tim	310	}
363